{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Claudia data CGI tracks"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "import pybedtools\n",
    "from os import listdir\n",
    "from Bio import SeqIO"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Import libraries and genome\n",
    "my_seqlist = []\n",
    "for seq_record in SeqIO.parse('genome/Mus_musculus.GRCm38.chromosome.1.fa', 'fasta'):\n",
    "    my_seqlist.append(seq_record)\n",
    "\n",
    "CpG_Ill = pybedtools.BedTool(\"CpG_Il_mm10.bed\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Total number of seqs\n",
      "66\n",
      "ID seq 1\n",
      "1\n",
      "First 100 bp seq 1\n",
      "NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n",
      "Total length seq 1\n",
      "195471971\n"
     ]
    }
   ],
   "source": [
    "print(\"Total number of seqs\")\n",
    "print(len(my_seqlist))\n",
    "print(\"ID seq 1\")\n",
    "print(my_seqlist[0].id)\n",
    "print(\"First 100 bp seq 1\")\n",
    "print(my_seqlist[0].seq[0:100])\n",
    "print(\"Total length seq 1\")\n",
    "print(len(my_seqlist[0]))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Obtain CG kmers list\n",
    "from itertools import product\n",
    "\n",
    "kmers = list(product('ATCG', repeat=6))\n",
    "kmers = [\"\".join(x) for x in kmers]\n",
    "\n",
    "kmers_CG = []\n",
    "for i in kmers:\n",
    "    if i[2:4] == \"CG\":\n",
    "        kmers_CG.append(i)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Dictionary key location\n",
    "dict_chr_loc = {}\n",
    "for i in range(len(my_seqlist)):\n",
    "    dict_chr_loc[my_seqlist[i].id] = i"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Function to analyze k-mers\n",
    "def kmer_analysis(file_name,folder_input,folder_output):    \n",
    "    file_input = str(folder_input) + \"/\"+ str(file_name)\n",
    "    print(file_input)\n",
    "    df = pd.read_csv(file_input,sep='\\t',skiprows=0,header=None, dtype={0: str})\n",
    "\n",
    "    pd_kmers_CG = pd.DataFrame(0, index=kmers_CG, columns=['Met','Unmet'])\n",
    "\n",
    "    for i in range(len(df)):\n",
    "        position = my_seqlist[dict_chr_loc.get(df[0][i])].seq[(df[1][i])-1]\n",
    "        if position == \"C\":\n",
    "            substring = my_seqlist[dict_chr_loc.get(df[0][i])].seq[(df[1][i])-3:df[1][i]+3]\n",
    "        elif position ==\"G\":\n",
    "            substring = (my_seqlist[dict_chr_loc.get(df[0][i])].seq[(df[1][i])-4:df[1][i]+2]).reverse_complement()\n",
    "        if (substring[2:4] == \"CG\") & (str(substring) in kmers_CG):\n",
    "            if df[3][i] == \"Z\":\n",
    "                pd_kmers_CG.loc[str(substring)][0] = (pd_kmers_CG.loc[str(substring)][0]) + 1\n",
    "            else:\n",
    "                pd_kmers_CG.loc[str(substring)][1] = (pd_kmers_CG.loc[str(substring)][1]) + 1\n",
    "\n",
    "    pd_kmers_CG['Total'] = pd_kmers_CG.sum(axis=1)\n",
    "    pd_kmers_CG['Per_met'] = pd_kmers_CG['Met']*100/pd_kmers_CG['Total']\n",
    "    file_output = str(folder_output) + \"/\" + str(file_name) + \".csv\"\n",
    "    pd_kmers_CG.to_csv(file_output) "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Claudia CGI analysis"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [],
   "source": [
    "files = listdir(\"Claudia\")\n",
    "inputs = []\n",
    "for i in range(len(files)):\n",
    "    if files[i].endswith(\"deduplicated.txt\") == True:\n",
    "        inputs.append(files[i])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CpG_context_50ugmL_Asc_2i_A_0h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_50ugmL_Asc_2i_A_12_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_50ugmL_Asc_2i_A_18h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_50ugmL_Asc_2i_A_24h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_50ugmL_Asc_2i_A_30h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_50ugmL_Asc_2i_A_36h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_50ugmL_Asc_2i_A_42h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_50ugmL_Asc_2i_A_6h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_50ugmL_Asc_2i_B_0h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_50ugmL_Asc_2i_B_12_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_50ugmL_Asc_2i_B_18h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_50ugmL_Asc_2i_B_24h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_50ugmL_Asc_2i_B_30h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_50ugmL_Asc_2i_B_36h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_50ugmL_Asc_2i_B_42h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_50ugmL_Asc_2i_B_6h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_50ugmL_Asc_2i_C_0h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_50ugmL_Asc_2i_C_12_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
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      "CpG_context_50ugmLAsc_C_12h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
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      "CpG_context_50ugmLAsc_DOX_2i_C_12h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_50ugmLAsc_DOX_2i_C_18_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_50ugmLAsc_DOX_2i_C_24h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/Users/oscarortega/anaconda/lib/python3.6/site-packages/IPython/core/interactiveshell.py:2717: DtypeWarning: Columns (2) have mixed types. Specify dtype option on import or set low_memory=False.\n",
      "  interactivity=interactivity, compiler=compiler, result=result)\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CpG_context_50ugmLAsc_DOX_2i_C_30h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_50ugmLAsc_DOX_2i_C_36h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
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      "CpG_context_iSeq008_50ugmLAsc_B_54h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_B_60h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_B_66h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_B_72h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_B_72h_serum_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_B_78h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_B_84h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_C_48h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_C_54h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_C_60h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_C_66h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_C_72h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_C_72h_serum_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_C_78h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_C_84h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_DOX_2i_A_48h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_DOX_2i_A_54h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_DOX_2i_A_60h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_DOX_2i_A_66h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_DOX_2i_A_72h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_DOX_2i_A_72h_serum_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_DOX_2i_A_78h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_DOX_2i_A_84h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_DOX_2i_B_48h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_DOX_2i_B_54h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_DOX_2i_B_60h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_DOX_2i_B_66h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_DOX_2i_B_72h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_DOX_2i_B_72h_serum_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_DOX_2i_B_78h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_DOX_2i_B_84h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_DOX_2i_C_48h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_DOX_2i_C_54h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_DOX_2i_C_60h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_DOX_2i_C_66h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_DOX_2i_C_72h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_DOX_2i_C_72h_serum_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_DOX_2i_C_78h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_DOX_2i_C_84h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_Dox_A_48h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_Dox_A_54h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_Dox_A_60h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_Dox_A_66h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_Dox_A_72h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_Dox_A_72h_serum_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_Dox_A_78h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_Dox_A_84h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_Dox_B_48h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_Dox_B_54h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_Dox_B_60h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_Dox_B_66h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_Dox_B_72h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_Dox_B_72h_serum_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_Dox_B_78h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_Dox_B_84h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_Dox_C_48h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_Dox_C_54h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_Dox_C_60h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_Dox_C_66h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_Dox_C_72h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_Dox_C_72h_serum_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_Dox_C_78h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n",
      "CpG_context_iSeq008_50ugmLAsc_Dox_C_84h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt\n"
     ]
    }
   ],
   "source": [
    "folder_input = \"Claudia/\"\n",
    "out_path = \"Claudia_CGI/\"\n",
    "\n",
    "for input_temp in inputs:\n",
    "    print(input_temp)\n",
    "    file_input = folder_input + input_temp\n",
    "    df = pd.read_csv(file_input,sep='\\t',skiprows=1,header=None)\n",
    "    list_positions = pd.DataFrame(df[[2,3,3,4]]).values.tolist()\n",
    "    temp_bed = pybedtools.BedTool(list_positions)\n",
    "    temp_CPI = (temp_bed.intersect(CpG_Ill))\n",
    "    temp_non_CPI = (temp_bed - temp_CPI)\n",
    "    \n",
    "    temp_CPI.saveas(out_path + \"CGI_\" + input_temp + \".csv\")\n",
    "    temp_non_CPI.saveas(out_path + \"non_CGI_\" + input_temp + \".csv\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [],
   "source": [
    "files = listdir(\"Claudia_CGI\")\n",
    "inputs = []\n",
    "for i in range(len(files)):\n",
    "    if files[i].endswith(\"deduplicated.txt.csv\") == True:\n",
    "        inputs.append(files[i])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Claudia_CGI/CGI_CpG_context_50ugmL_Asc_2i_A_0h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmL_Asc_2i_A_12_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmL_Asc_2i_A_18h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmL_Asc_2i_A_24h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmL_Asc_2i_A_30h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmL_Asc_2i_A_36h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmL_Asc_2i_A_42h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmL_Asc_2i_A_6h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmL_Asc_2i_B_0h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmL_Asc_2i_B_12_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmL_Asc_2i_B_18h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmL_Asc_2i_B_24h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmL_Asc_2i_B_30h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmL_Asc_2i_B_36h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmL_Asc_2i_B_42h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmL_Asc_2i_B_6h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmL_Asc_2i_C_0h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmL_Asc_2i_C_12_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmL_Asc_2i_C_18h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmL_Asc_2i_C_24h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmL_Asc_2i_C_30h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmL_Asc_2i_C_36h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmL_Asc_2i_C_42h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmL_Asc_2i_C_6h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmLAsc_A_0h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmLAsc_A_12h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmLAsc_A_18h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmLAsc_A_24h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmLAsc_A_30h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmLAsc_A_36h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmLAsc_A_42h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmLAsc_A_6h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmLAsc_B_0h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmLAsc_B_12h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmLAsc_B_24h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmLAsc_B_30h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmLAsc_B_42h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmLAsc_B_6h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmLAsc_C_0h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmLAsc_C_12h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmLAsc_C_24h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmLAsc_C_30h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmLAsc_C_42h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmLAsc_C_6h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmLAsc_DOX_2i_A_0h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmLAsc_DOX_2i_A_12h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmLAsc_DOX_2i_A_18_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmLAsc_DOX_2i_A_24h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmLAsc_DOX_2i_A_30h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmLAsc_DOX_2i_A_36h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmLAsc_DOX_2i_A_42h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmLAsc_DOX_2i_A_6h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmLAsc_DOX_2i_B_0h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmLAsc_DOX_2i_B_12h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmLAsc_DOX_2i_B_18_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmLAsc_DOX_2i_B_24h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmLAsc_DOX_2i_B_30h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmLAsc_DOX_2i_B_36h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmLAsc_DOX_2i_B_42h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmLAsc_DOX_2i_B_6h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmLAsc_DOX_2i_C_0h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmLAsc_DOX_2i_C_12h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmLAsc_DOX_2i_C_18_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmLAsc_DOX_2i_C_24h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmLAsc_DOX_2i_C_30h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmLAsc_DOX_2i_C_36h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmLAsc_DOX_2i_C_42h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmLAsc_DOX_2i_C_6h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmLAsc_Dox_A_0h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmLAsc_Dox_A_12h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmLAsc_Dox_A_18h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmLAsc_Dox_A_24h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmLAsc_Dox_A_30h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/CGI_CpG_context_50ugmLAsc_Dox_A_36h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
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      "Claudia_CGI/non_CGI_CpG_context_iSeq008_50ugmLAsc_DOX_2i_A_72h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/non_CGI_CpG_context_iSeq008_50ugmLAsc_DOX_2i_A_72h_serum_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/non_CGI_CpG_context_iSeq008_50ugmLAsc_DOX_2i_A_78h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/non_CGI_CpG_context_iSeq008_50ugmLAsc_DOX_2i_A_84h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/non_CGI_CpG_context_iSeq008_50ugmLAsc_DOX_2i_B_48h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/non_CGI_CpG_context_iSeq008_50ugmLAsc_DOX_2i_B_54h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/non_CGI_CpG_context_iSeq008_50ugmLAsc_DOX_2i_B_60h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/non_CGI_CpG_context_iSeq008_50ugmLAsc_DOX_2i_B_66h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/non_CGI_CpG_context_iSeq008_50ugmLAsc_DOX_2i_B_72h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/non_CGI_CpG_context_iSeq008_50ugmLAsc_DOX_2i_B_72h_serum_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/non_CGI_CpG_context_iSeq008_50ugmLAsc_DOX_2i_B_78h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/non_CGI_CpG_context_iSeq008_50ugmLAsc_DOX_2i_B_84h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/non_CGI_CpG_context_iSeq008_50ugmLAsc_DOX_2i_C_48h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/non_CGI_CpG_context_iSeq008_50ugmLAsc_DOX_2i_C_54h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/non_CGI_CpG_context_iSeq008_50ugmLAsc_DOX_2i_C_60h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/non_CGI_CpG_context_iSeq008_50ugmLAsc_DOX_2i_C_66h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/non_CGI_CpG_context_iSeq008_50ugmLAsc_DOX_2i_C_72h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/non_CGI_CpG_context_iSeq008_50ugmLAsc_DOX_2i_C_72h_serum_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/non_CGI_CpG_context_iSeq008_50ugmLAsc_DOX_2i_C_78h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/non_CGI_CpG_context_iSeq008_50ugmLAsc_DOX_2i_C_84h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/non_CGI_CpG_context_iSeq008_50ugmLAsc_Dox_A_48h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/non_CGI_CpG_context_iSeq008_50ugmLAsc_Dox_A_54h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/non_CGI_CpG_context_iSeq008_50ugmLAsc_Dox_A_60h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/non_CGI_CpG_context_iSeq008_50ugmLAsc_Dox_A_66h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/non_CGI_CpG_context_iSeq008_50ugmLAsc_Dox_A_72h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/non_CGI_CpG_context_iSeq008_50ugmLAsc_Dox_A_72h_serum_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/non_CGI_CpG_context_iSeq008_50ugmLAsc_Dox_A_78h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/non_CGI_CpG_context_iSeq008_50ugmLAsc_Dox_A_84h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/non_CGI_CpG_context_iSeq008_50ugmLAsc_Dox_B_48h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/non_CGI_CpG_context_iSeq008_50ugmLAsc_Dox_B_54h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/non_CGI_CpG_context_iSeq008_50ugmLAsc_Dox_B_60h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/non_CGI_CpG_context_iSeq008_50ugmLAsc_Dox_B_66h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/non_CGI_CpG_context_iSeq008_50ugmLAsc_Dox_B_72h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/non_CGI_CpG_context_iSeq008_50ugmLAsc_Dox_B_72h_serum_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/non_CGI_CpG_context_iSeq008_50ugmLAsc_Dox_B_78h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/non_CGI_CpG_context_iSeq008_50ugmLAsc_Dox_B_84h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/non_CGI_CpG_context_iSeq008_50ugmLAsc_Dox_C_48h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/non_CGI_CpG_context_iSeq008_50ugmLAsc_Dox_C_54h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/non_CGI_CpG_context_iSeq008_50ugmLAsc_Dox_C_60h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/non_CGI_CpG_context_iSeq008_50ugmLAsc_Dox_C_66h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/non_CGI_CpG_context_iSeq008_50ugmLAsc_Dox_C_72h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/non_CGI_CpG_context_iSeq008_50ugmLAsc_Dox_C_72h_serum_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/non_CGI_CpG_context_iSeq008_50ugmLAsc_Dox_C_78h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Claudia_CGI/non_CGI_CpG_context_iSeq008_50ugmLAsc_Dox_C_84h_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n"
     ]
    }
   ],
   "source": [
    "for i in range(len(inputs)):\n",
    "    kmer_analysis(inputs[i],\"Claudia_CGI\",\"Claudia_CGI_output\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Rosie CGI analysis"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "metadata": {},
   "outputs": [],
   "source": [
    "files = listdir(\"Rosie\")\n",
    "inputs = []\n",
    "for i in range(len(files)):\n",
    "    if files[i].endswith(\"deduplicated.txt\") == True:\n",
    "        inputs.append(files[i])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 34,
   "metadata": {},
   "outputs": [],
   "source": [
    "folder_input = \"Rosie/\"\n",
    "out_path = \"Rosie_CGI/\"\n",
    "\n",
    "for input_temp in inputs:\n",
    "    file_input = folder_input + input_temp\n",
    "    df = pd.read_csv(file_input,sep='\\t',skiprows=1,header=None)\n",
    "    list_positions = pd.DataFrame(df[[2,3,3,4]]).values.tolist()\n",
    "    temp_bed = pybedtools.BedTool(list_positions)\n",
    "    temp_CPI = (temp_bed.intersect(CpG_Ill))\n",
    "    temp_non_CPI = (temp_bed - temp_CPI)\n",
    "    \n",
    "    temp_CPI.saveas(out_path + \"CGI_\" + input_temp + \".csv\")\n",
    "    temp_non_CPI.saveas(out_path + \"non_CGI_\" + input_temp + \".csv\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 35,
   "metadata": {},
   "outputs": [],
   "source": [
    "files = listdir(\"Rosie_CGI\")\n",
    "inputs = []\n",
    "for i in range(len(files)):\n",
    "    if files[i].endswith(\"deduplicated.txt.csv\") == True:\n",
    "        inputs.append(files[i])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 38,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Rosie_CGI/CGI_CpG_context_iSeq009_TET_TKO_5AZA_0h_R1_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_TET_TKO_5AZA_0h_R2_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_TET_TKO_5AZA_0h_R3_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_TET_TKO_5AZA_12h_R1_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_TET_TKO_5AZA_12h_R2_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_TET_TKO_5AZA_12h_R3_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_TET_TKO_5AZA_18h_R1_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_TET_TKO_5AZA_18h_R2_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_TET_TKO_5AZA_18h_R3_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_TET_TKO_5AZA_6h_R1_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_TET_TKO_5AZA_6h_R2_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_TET_TKO_5AZA_6h_R3_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_V65_5AZA_0h_R1_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_V65_5AZA_0h_R2_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_V65_5AZA_0h_R3_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_V65_5AZA_12h_R1_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_V65_5AZA_12h_R2_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_V65_5AZA_12h_R3_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_V65_5AZA_18h_R1_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_V65_5AZA_18h_R2_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_V65_5AZA_18h_R3_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_V65_5AZA_24h_R1_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_V65_5AZA_24h_R2_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_V65_5AZA_24h_R3_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_V65_5AZA_30h_R1_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_V65_5AZA_30h_R2_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_V65_5AZA_30h_R3_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_V65_5AZA_36h_R1_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_V65_5AZA_36h_R2_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_V65_5AZA_36h_R3_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_V65_5AZA_42h_R1_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_V65_5AZA_42h_R2_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_V65_5AZA_42h_R3_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_V65_5AZA_48h_R1_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_V65_5AZA_48h_R2_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_V65_5AZA_48h_R3_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_V65_5AZA_6h_R1_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_V65_5AZA_6h_R2_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_V65_5AZA_6h_R3_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_V65_negative_0h_R1_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_V65_negative_0h_R2_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_V65_negative_0h_R3_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_V65_negative_12h_R1_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_V65_negative_12h_R2_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_V65_negative_12h_R3_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_V65_negative_18h_R1_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_V65_negative_18h_R2_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_V65_negative_18h_R3_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_V65_negative_24h_R1_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_V65_negative_24h_R2_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_V65_negative_24h_R3_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_V65_negative_30h_R1_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_V65_negative_30h_R2_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_V65_negative_30h_R3_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_V65_negative_36h_R1_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_V65_negative_36h_R2_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_V65_negative_36h_R3_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_V65_negative_42h_R1_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_V65_negative_42h_R2_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_V65_negative_42h_R3_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_V65_negative_48h_R1_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_V65_negative_48h_R2_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_V65_negative_48h_R3_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_V65_negative_6h_R1_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_V65_negative_6h_R2_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/CGI_CpG_context_iSeq009_V65_negative_6h_R3_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_TET_TKO_5AZA_0h_R1_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_TET_TKO_5AZA_0h_R2_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_TET_TKO_5AZA_0h_R3_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_TET_TKO_5AZA_12h_R1_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_TET_TKO_5AZA_12h_R2_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_TET_TKO_5AZA_12h_R3_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_TET_TKO_5AZA_18h_R1_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_TET_TKO_5AZA_18h_R2_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_TET_TKO_5AZA_18h_R3_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_TET_TKO_5AZA_6h_R1_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_TET_TKO_5AZA_6h_R2_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_TET_TKO_5AZA_6h_R3_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_V65_5AZA_0h_R1_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_V65_5AZA_0h_R2_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_V65_5AZA_0h_R3_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_V65_5AZA_12h_R1_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_V65_5AZA_12h_R2_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_V65_5AZA_12h_R3_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_V65_5AZA_18h_R1_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_V65_5AZA_18h_R2_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_V65_5AZA_18h_R3_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_V65_5AZA_24h_R1_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_V65_5AZA_24h_R2_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_V65_5AZA_24h_R3_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_V65_5AZA_30h_R1_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_V65_5AZA_30h_R2_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_V65_5AZA_30h_R3_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_V65_5AZA_36h_R1_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_V65_5AZA_36h_R2_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_V65_5AZA_36h_R3_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_V65_5AZA_42h_R1_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_V65_5AZA_42h_R2_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_V65_5AZA_42h_R3_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_V65_5AZA_48h_R1_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_V65_5AZA_48h_R2_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_V65_5AZA_48h_R3_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_V65_5AZA_6h_R1_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_V65_5AZA_6h_R2_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_V65_5AZA_6h_R3_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_V65_negative_0h_R1_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_V65_negative_0h_R2_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_V65_negative_0h_R3_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_V65_negative_12h_R1_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_V65_negative_12h_R2_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_V65_negative_12h_R3_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_V65_negative_18h_R1_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_V65_negative_18h_R2_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_V65_negative_18h_R3_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_V65_negative_24h_R1_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_V65_negative_24h_R2_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_V65_negative_24h_R3_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_V65_negative_30h_R1_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_V65_negative_30h_R2_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_V65_negative_30h_R3_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_V65_negative_36h_R1_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_V65_negative_36h_R2_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_V65_negative_36h_R3_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_V65_negative_42h_R1_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_V65_negative_42h_R2_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_V65_negative_42h_R3_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_V65_negative_48h_R1_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_V65_negative_48h_R2_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_V65_negative_48h_R3_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_V65_negative_6h_R1_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_V65_negative_6h_R2_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n",
      "Rosie_CGI/non_CGI_CpG_context_iSeq009_V65_negative_6h_R3_RG_fastq.gz_trimmed_bismark_bt2.deduplicated.txt.csv\n"
     ]
    }
   ],
   "source": [
    "for i in range(len(inputs)):\n",
    "    kmer_analysis(inputs[i],\"Rosie_CGI\",\"Rosie_CGI_output\")"
   ]
  }
 ],
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